Locus 3747

Sequence ID 3R_DroMel_CAF1
Location 10,164,404 – 10,164,495
Length 91
Max. P 0.729023
window6005 window6006

overview

Window 5

Location 10,164,404 – 10,164,495
Length 91
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 77.02
Mean single sequence MFE -29.02
Consensus MFE -10.97
Energy contribution -11.38
Covariance contribution 0.42
Combinations/Pair 1.20
Mean z-score -2.42
Structure conservation index 0.38
SVM decision value 0.42
SVM RNA-class probability 0.729023
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10164404 91 + 27905053
GAGUG---GUGGGUCGAUGGGAAAAUUGGCAAGUGCCAAUGCAAAUGGCCAAAAGGCUUAAUGUCCGG---CCACAGCAGGAUACCCACAUACACAA
..(((---((((((..........((((((....))))))((...(((((....(((.....))).))---)))..)).....)))))).))).... ( -30.50)
>DroPse_CAF1 25001 90 + 1
GUGU---GGGCGGUCAAUGGGAAAAUUGGCAAGUGCCAAUGCAAAUGGCCGAGAGGCUUAAUG-CUGG---CCACAGCAGGAUACACGCACACGAGA
((((---(.(.(((((((......))))))..((((((..(((...((((....))))...))-))))---.))).........).).))))).... ( -33.50)
>DroSim_CAF1 21959 94 + 1
GAGUGGCGGUGGGUCGAUGGGAAAAUUGGCAAGUGCCAAUGCAAAUGGCCAAAAGGCUUAAUGUCCGG---UCACAGCAGGAUACCCACAUACACAA
..(((...((((((.(((.(((..((((((....)))))).((...((((....))))...))))).)---)).(....)...))))))...))).. ( -33.20)
>DroWil_CAF1 27285 81 + 1
--------------CAGUGGGAAAAUGAGCAAGUGCCAAUGCAAAUGACCAAAAGGCUUAAGGCCCAAGCUACACAGCAGAAUGCACAAACACUU--
--------------.((((......((.((....)))).((((...........(((.....)))...(((....)))....))))....)))).-- ( -15.20)
>DroAna_CAF1 21811 89 + 1
CAGCGGC----UGUCGAUGGGAAAAUUGGCAAGUGCCAAUGCAAAUGACCAGGAGGCUUAAUG-CCGG---CCACAGCAGGAUCCGCUCACACAAGC
.((((((----(((.(.(((....((((((....))))))........)))((.(((.....)-))..---)).).))))...)))))......... ( -28.20)
>DroPer_CAF1 25379 90 + 1
GUGU---GGGCGGUCAAUGGGAAAAUUGGCAAGUGCCAAUGCAAAUGGCCGAGAGGCUUAAUG-CUGG---CCACAGCAGGAUACACGCACACGAGA
((((---(.(.(((((((......))))))..((((((..(((...((((....))))...))-))))---.))).........).).))))).... ( -33.50)
>consensus
GAGU____G__GGUCAAUGGGAAAAUUGGCAAGUGCCAAUGCAAAUGGCCAAAAGGCUUAAUG_CCGG___CCACAGCAGGAUACACACACACAAGA
...........(((((....(...((((((....)))))).)...)))))....(((.....).))............................... (-10.97 = -11.38 +   0.42)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,164,404 – 10,164,495
Length 91
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 77.02
Mean single sequence MFE -26.98
Consensus MFE -10.83
Energy contribution -10.83
Covariance contribution 0.00
Combinations/Pair 1.21
Mean z-score -2.13
Structure conservation index 0.40
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10164404 91 - 27905053
UUGUGUAUGUGGGUAUCCUGCUGUGG---CCGGACAUUAAGCCUUUUGGCCAUUUGCAUUGGCACUUGCCAAUUUUCCCAUCGACCCAC---CACUC
..(((...((((((.....((.((((---(((((..........)))))))))..))((((((....))))))..........))))))---))).. ( -31.80)
>DroPse_CAF1 25001 90 - 1
UCUCGUGUGCGUGUAUCCUGCUGUGG---CCAG-CAUUAAGCCUCUCGGCCAUUUGCAUUGGCACUUGCCAAUUUUCCCAUUGACCGCCC---ACAC
....(((.(((.((.....((.((((---((.(-(.....)).....))))))..))((((((....))))))..........))))).)---)).. ( -28.10)
>DroSim_CAF1 21959 94 - 1
UUGUGUAUGUGGGUAUCCUGCUGUGA---CCGGACAUUAAGCCUUUUGGCCAUUUGCAUUGGCACUUGCCAAUUUUCCCAUCGACCCACCGCCACUC
..(((...((((((.....((.(((.---(((((..........))))).)))..))((((((....))))))..........))))))...))).. ( -25.90)
>DroWil_CAF1 27285 81 - 1
--AAGUGUUUGUGCAUUCUGCUGUGUAGCUUGGGCCUUAAGCCUUUUGGUCAUUUGCAUUGGCACUUGCUCAUUUUCCCACUG--------------
--..(.((..((((....(((...((..((.((((.....))))...))..))..)))...))))..)).)............-------------- ( -19.70)
>DroAna_CAF1 21811 89 - 1
GCUUGUGUGAGCGGAUCCUGCUGUGG---CCGG-CAUUAAGCCUCCUGGUCAUUUGCAUUGGCACUUGCCAAUUUUCCCAUCGACA----GCCGCUG
.........(((((.....((.((((---((((-(.....)))....))))))..))((((((....)))))).............----.))))). ( -28.30)
>DroPer_CAF1 25379 90 - 1
UCUCGUGUGCGUGUAUCCUGCUGUGG---CCAG-CAUUAAGCCUCUCGGCCAUUUGCAUUGGCACUUGCCAAUUUUCCCAUUGACCGCCC---ACAC
....(((.(((.((.....((.((((---((.(-(.....)).....))))))..))((((((....))))))..........))))).)---)).. ( -28.10)
>consensus
UCUUGUGUGUGUGUAUCCUGCUGUGG___CCGG_CAUUAAGCCUCUUGGCCAUUUGCAUUGGCACUUGCCAAUUUUCCCAUCGACC__C____ACUC
....................(.((((..............(((....))).......((((((....))))))....)))).).............. (-10.83 = -10.83 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:04 2006